utils¶
This module provides several utility functions to be used within the SNP-IC and cpSNP-IC calculation pipelines. It exposes both a Click CLI group and Python-callable wrappers.
CLI Commands¶
oddSNP utils¶
Usage
oddSNP utils [OPTIONS] COMMAND [ARGS]...
count-lines¶
Count the number of lines in a BAM file using samtools
Arguments:
BAM: Name of the BAM file
Usage
oddSNP utils count-lines [OPTIONS] BAM
Options
- --nproc <nproc>¶
Number of parallel processes to use
Arguments
- BAM¶
Required argument
cslite-pileup¶
Run cellsnp-lite to generate pileup files
Arguments:
BAM: input bam file
REFERENCE: List of reference variants
BARCODES: List of cell barcodes
OUPATH: Path to directory to store results.
Usage
oddSNP utils cslite-pileup [OPTIONS] BAM REFERENCE BARCODES OUPATH
Options
- --celltag <celltag>¶
Tag used to reference cell barcodes in the BAM.
- --umitag <umitag>¶
Tag used to reference UMI codes in the BAM.
- --mincount <mincount>¶
- --nproc <nproc>¶
Number of processes to use
- --force¶
Override previous results
Arguments
- BAM¶
Required argument
- REFERENCE¶
Required argument
- BARCODES¶
Required argument
- OUPATH¶
Required argument
vireo¶
Run vireo to demultiplex single-cell data based on genotype information.
Arguments:
INPATH: Path to the input file containing the single-cell data to be demultiplexed.
OUPATH: Path to the output directory to store results.
Usage
oddSNP utils vireo [OPTIONS] INPATH OUPATH
Options
- --genotype <genotype>¶
Path to the donors genotype VCF file.
- --genotag <genotag>¶
Genotype tag to use from the VCF file (GT, GP, or PL). Default is PL.
- --ndonor <ndonor>¶
Number of donors in the sample. If not provided, vireo will try to estimate it automatically.
- --nproc <nproc>¶
Number of parallel processes to use
- --force¶
Override target files.
Arguments
- INPATH¶
Required argument
- OUPATH¶
Required argument
Python API¶
- oddSNP.utils.assert_cellsnplite()[source]¶
Asserts that cellsnp-slite has been installed and executable.
- oddSNP.utils.call_count_lines(bam, nproc)[source]¶
Python wrapper for
count_lines().- Parameters:
bam – The BAM file to process
nproc – Number of parallel processes to use
- Returns:
The number of lines in the BAM file as an integer
- oddSNP.utils.call_cslite_pileup(bam, reference, barcodes, oupath, celltag, umitag, mincount, nproc, force)[source]¶
Python wrapper for
cslite_pileup().- Parameters:
bam – The BAM file to process
reference – List of reference variants
barcodes – List of cell barcodes
oupath – Path to directory to store results
celltag – Tag used to reference cell barcodes in the BAM
umitag – Tag used to reference UMI codes in the BAM
mincount – Minimum count threshold for pileup
nproc – Number of processes to use
force – If True overwrites existing results
- Returns:
None
- oddSNP.utils.call_vireo(inpath, oupath, genotype, genotag, ndonor, nproc, force)[source]¶
Python wrapper for
vireo()- Parameters:
inpath – Path to the input file containing the single-cell data to be demultiplexed.
oupath – Path to the output directory to store results.
genotype – Path to the donors genotype VCF file.
genotag – Genotype tag to use from the VCF file (GT, GP, or PL). Default is PL.
ndonor – Number of donors in the sample. If not provided, vireo will try to estimate it automatically.
nproc – Number of parallel processes to use
force – If True overwrites existing results